update kindling to new rendering framework, and fix many bugs

build.gradle.kts

@@ -7,7 +7,7 @@ plugins {
 }
 
 group = "org.hl7.fhir"
-version = "1.9.2-SNAPSHOT"
+version = "1.9.3-SNAPSHOT"
 
 java {
     withJavadocJar()

gradle.properties

@@ -1,4 +1,4 @@
-fhirCoreVersion = 6.3.2
+fhirCoreVersion = 6.3.19
 apachePoiVersion = 5.2.1
 jacksonVersion = 2.16.0
 apacheHttpcomponentsVersion = 4.5.13

src/main/java/org/hl7/fhir/definitions/generators/specification/DataTypeTableGenerator.java

@@ -5,6 +5,7 @@
 import org.hl7.fhir.definitions.model.ElementDefn;
 import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
 import org.hl7.fhir.tools.publisher.PageProcessor;
+import org.hl7.fhir.utilities.i18n.RenderingI18nContext;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
@@ -16,7 +17,7 @@ public DataTypeTableGenerator(String dest, PageProcessor page, String pageName,
   }
 
   public XhtmlNode generate(ElementDefn e, Set<String> outputTracker, boolean isActive) throws Exception {
-    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(dest, inlineGraphics, false);
+    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(new RenderingI18nContext(), dest, inlineGraphics, false);
     TableModel model = gen.initNormalTable("", false, true, e.getName(), isActive, isActive ? TableGenerationMode.XHTML : TableGenerationMode.XML);
 
     model.getRows().add(genElement(e, gen, false, e.getName(), false, "", RenderMode.DATATYPE, true, e.getStandardsStatus(), null, e.isAbstractType(), false));

src/main/java/org/hl7/fhir/definitions/generators/specification/ProfileGenerator.java

@@ -76,6 +76,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.r5.conformance.profile.ProfileKnowledgeProvider;
 import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
+import org.hl7.fhir.r5.context.ContextUtilities;
 import org.hl7.fhir.r5.formats.FormatUtilities;
 import org.hl7.fhir.r5.model.BooleanType;
 import org.hl7.fhir.r5.model.Bundle;
@@ -138,6 +139,7 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.r5.model.UriType;
 import org.hl7.fhir.r5.renderers.OperationDefinitionRenderer;
 import org.hl7.fhir.r5.renderers.utils.RenderingContext;
+import org.hl7.fhir.r5.renderers.utils.ResourceWrapper;
 import org.hl7.fhir.r5.utils.BuildExtensions;
 import org.hl7.fhir.r5.utils.CanonicalResourceUtilities;
 import org.hl7.fhir.r5.utils.ToolingExtensions;
@@ -2601,7 +2603,7 @@ else if (op.getKind().toLowerCase().equals("query"))
       produceOpParam(op.getName(), opd.getParameter(), p, null);
     }
     OperationDefinitionRenderer opr = new OperationDefinitionRenderer(rc);
-    opr.render(opd);
+    opr.renderResource(ResourceWrapper.forResource(new ContextUtilities(context), opd));
     return opd;
   }
 

src/main/java/org/hl7/fhir/definitions/generators/specification/ResourceDependencyGenerator.java

@@ -18,6 +18,7 @@
 import org.hl7.fhir.tools.publisher.PageProcessor;
 import org.hl7.fhir.utilities.StandardsStatus;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.i18n.RenderingI18nContext;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
@@ -49,7 +50,7 @@ public ResourceDependencyGenerator(String dest, PageProcessor page, String pageN
   }
 
   public XhtmlNode generate(ElementDefn e, String prefix) throws Exception {
-    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(dest, inlineGraphics, true);
+    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(new RenderingI18nContext(), dest, inlineGraphics, true);
     RenderMode mode = RenderMode.RESOURCE;
     TableModel model = initTable(gen, prefix, mode == RenderMode.LOGICAL, e.getName());
 

src/main/java/org/hl7/fhir/definitions/generators/specification/ResourceTableGenerator.java

@@ -4,6 +4,7 @@
 import org.hl7.fhir.definitions.model.ResourceDefn;
 import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
 import org.hl7.fhir.tools.publisher.PageProcessor;
+import org.hl7.fhir.utilities.i18n.RenderingI18nContext;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
 import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
@@ -16,7 +17,7 @@ public ResourceTableGenerator(String dest, PageProcessor page, String pageName,
   }
 
   public XhtmlNode generate(ResourceDefn r, String prefix, boolean isActive) throws Exception {
-    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(dest, inlineGraphics, true);
+    HierarchicalTableGenerator gen = new HierarchicalTableGenerator(new RenderingI18nContext(), dest, inlineGraphics, true);
     ElementDefn e = r.getRoot();
     RenderMode mode = e.typeCode().equals("Logical") && hasLogicalMapping(e) ? RenderMode.LOGICAL : RenderMode.RESOURCE;
     TableModel model = gen.initNormalTable(prefix, mode == RenderMode.LOGICAL, true, r.getName(), isActive, isActive ? TableGenerationMode.XHTML : TableGenerationMode.XML);

src/main/java/org/hl7/fhir/definitions/generators/specification/SDUsageMapper.java

@@ -112,17 +112,19 @@ private void process(String name, String path, Element resource) {
   }
 
   private void walkChildren(String name, String path, Element element) {
-    for (Element ex : element.getChildren("extension")) {
-      see(name, path, ex.getNamedChildValue("url"));
-    }
-    for (Element ex : element.getChildren("modifierExtension")) {
-      see(name, path, ex.getNamedChildValue("url"));
-    }
-    for (Element c : element.getChildren()) {
-      if (c.isResource()) {
-        process(name, path, c); 
-      } else if (!c.isPrimitive()) {
-        walkChildren(name, path, c);
+    if (element.hasChildren()) {
+      for (Element ex : element.getChildren("extension")) {
+        see(name, path, ex.getNamedChildValue("url"));
+      }
+      for (Element ex : element.getChildren("modifierExtension")) {
+        see(name, path, ex.getNamedChildValue("url"));
+      }
+      for (Element c : element.getChildren()) {
+        if (c.isResource()) {
+          process(name, path, c); 
+        } else if (!c.isPrimitive()) {
+          walkChildren(name, path, c);
+        }
       }
     }
   }

src/main/java/org/hl7/fhir/definitions/generators/specification/json/SchemaGenerator.java

@@ -41,10 +41,10 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.definitions.model.TypeRef;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.tools.publisher.BuildWorkerContext;
-import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;

src/main/java/org/hl7/fhir/definitions/generators/xsd/SchemaGenerator.java

@@ -42,10 +42,10 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import org.hl7.fhir.definitions.model.Definitions;
 import org.hl7.fhir.definitions.model.ResourceDefn;
 import org.hl7.fhir.tools.publisher.BuildWorkerContext;
-import org.hl7.fhir.utilities.CSFile;
 import org.hl7.fhir.utilities.IniFile;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
 
 public class SchemaGenerator {
 

src/main/java/org/hl7/fhir/definitions/model/Example.java

@@ -30,7 +30,10 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 
  */
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -39,14 +42,17 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 
+import org.hl7.fhir.r5.context.IWorkerContext;
 import org.hl7.fhir.r5.elementmodel.Element;
+import org.hl7.fhir.r5.elementmodel.Manager;
+import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
 import org.hl7.fhir.r5.model.Resource;
 import org.hl7.fhir.tools.publisher.PageProcessor;
-import org.hl7.fhir.utilities.CSFile;
-import org.hl7.fhir.utilities.CSFileInputStream;
 import org.hl7.fhir.utilities.CSVProcessor;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.filesystem.CSFile;
+import org.hl7.fhir.utilities.filesystem.CSFileInputStream;
 import org.hl7.fhir.utilities.validation.ValidationMessage;
 import org.hl7.fhir.utilities.xml.XMLUtil;
 import org.w3c.dom.Document;
@@ -62,14 +68,16 @@ public class Example {
   private String xhtm;
   private ExampleType type;
   private boolean registered;
-  private Document xml;
   private String resourceName;
   private Set<Example> inbounds = new HashSet<Example>();
   private String ig;
   private String exampleFor;
   private Element element;
   private List<ValidationMessage> errors = new ArrayList<>();
   private Resource resource;
+  private IWorkerContext context;
+  private File path;
+  private boolean noId;
 
 
   public enum ExampleType {
@@ -80,35 +88,42 @@ public enum ExampleType {
   }
 
 
-  public Example(String name, String id, String title, String description, boolean registered, ExampleType type, Document doc) throws Exception {
+  public Example(String name, String id, String title, String description, boolean registered, ExampleType type, Element element) throws Exception {
     this.name = name;
     this.id = id;
     this.description = description;
     this.type = type;
     this.registered = registered;
     this.title = title;
+    this.element = element;
 
-    xml = doc;
-    resourceName = xml.getDocumentElement().getNodeName();
-    if (XMLUtil.getNamedChild(xml.getDocumentElement(), "id") == null)
+    resourceName = element.fhirType();
+    String xid = element.getIdBase();
+    if (xid == null)
       throw new Exception("no id element (looking for '"+id+"' from example "+id);
-    String xid = XMLUtil.getNamedChild(xml.getDocumentElement(), "id").getAttribute("value");
     if (!id.equals(xid)) {
       throw new Exception("misidentified resource example "+id+" expected '"+id+"' found '"+xid+"'");
     }
   }
 
 
-  public Example(String name, String id, String description, File path, boolean registered, ExampleType type, boolean noId) throws Exception {
+  public Example(IWorkerContext context, String name, String id, String description, File path, boolean registered, ExampleType type, boolean noId) throws Exception {
     super();
     this.name = name;
     this.id = id;
     this.description = description;
-    //    this.path = path;
+    this.path = path;
     this.type = type;
     this.registered = registered;
     this.title = getFileTitle(path);
+    this.context = context;
+    this.noId = noId;
+
+  }
 
+
+  private void loadExample()
+      throws FileNotFoundException, IOException, UnsupportedEncodingException, Exception {
     if( type == ExampleType.CsvFile ) {
       CSVProcessor csv = new CSVProcessor();
       csv.setSource(new CSFileInputStream(path));
@@ -120,23 +135,20 @@ public Example(String name, String id, String description, File path, boolean re
     }
 
     if (type == ExampleType.XmlFile || type == ExampleType.CsvFile || type == ExampleType.Container) {
-      DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
-      factory.setNamespaceAware(true);
       try {
-        DocumentBuilder builder = factory.newDocumentBuilder();
         String xs = TextFile.fileToString(new CSFile(path.getAbsolutePath()));
         xs = xs.replace("[%test-server%]", PageProcessor.TEST_SERVER_URL);
-        xml = builder.parse(new ByteArrayInputStream(xs.getBytes(Charsets.UTF_8)));
-        resourceName = xml.getDocumentElement().getNodeName();
+        element = Manager.parseSingle(context, new ByteArrayInputStream(xs.getBytes(Charsets.UTF_8)), FhirFormat.XML);
+        resourceName = element.fhirType();
       } catch (Exception e) {
         throw new Exception("unable to read "+path.getAbsolutePath()+": "+e.getMessage(), e);
       }
     }
-    if (xml != null && !noId) {
+    if (element != null && !noId) {
       if (!Utilities.noString(id)) {
-        if (XMLUtil.getNamedChild(xml.getDocumentElement(), "id") == null)
+        String xid = element.getIdBase();
+        if (xid == null)
           throw new Exception("no id element (looking for '"+id+"' from "+path.getName());
-        String xid = XMLUtil.getNamedChild(xml.getDocumentElement(), "id").getAttribute("value");
         if (!id.equals(xid)) {
           throw new Exception("misidentified resource "+path+" expected '"+id+"' found '"+xid+"'");
         }
@@ -191,9 +203,6 @@ public String getTitle() {
     return title;
   }
 
-  public Document getXml() {
-    return xml;
-  }
 
   public boolean isRegistered() {
     return registered;
@@ -237,7 +246,11 @@ public String getExampleFor() {
   }
 
 
-  public Element getElement() {
+  public Element getElement() throws FileNotFoundException, UnsupportedEncodingException, IOException, Exception {   
+    if (element == null) {
+      loadExample();
+    }
+
     return element;
   }
 
@@ -247,40 +260,42 @@ public void setElement(Element element) {
   }
 
 
-  public boolean hasXml() {
-    return xml != null;
-  }
-
-
   public List<ValidationMessage> getErrors() {
     return errors;
   }
 
 
-  public boolean hasContained() {
-    if (xml == null) {
-      return false;
+  public boolean hasContained() throws FileNotFoundException, UnsupportedEncodingException, IOException, Exception {
+    if (element == null) {
+      loadExample();
     }
-    Node n = xml.getDocumentElement().getFirstChild();
-    while (n != null && !"contained".equals(n.getNodeName())) {
-      n = n.getNextSibling();      
+
+    if (element == null) {
+      return false;
     }
-    return n != null;
+    return element.hasChildren("contained");
   }
 
 
-  public String getURL() {
-    return xml != null ? XMLUtil.getNamedChildValue(xml.getDocumentElement(), "url") : null;
+  public String getURL() throws FileNotFoundException, UnsupportedEncodingException, IOException, Exception {
+    if (element == null) {
+      loadExample();
+    }
+
+    if (element == null) {
+      return null;
+    }
+    return element.getNamedChildValue("url");
   }
 
 
   public String getOID() {
-    if (xml == null) {
+    if (element == null) {
       return null;
     }
-    for (org.w3c.dom.Element id : XMLUtil.getNamedChildren(xml.getDocumentElement(), "identifier")) {
-      String system = XMLUtil.getNamedChildValue(id, "system");
-      String value = XMLUtil.getNamedChildValue(id, "value");
+    for (Element id : element.getChildren("identifier")) {
+      String system = id.getNamedChildValue("system");
+      String value = id.getNamedChildValue("value");
       if ("urn:ietf:rfc:3986".equals(system) && value != null && value.startsWith("urn:oid:")) {
         return value.substring(8);
       }
@@ -304,4 +319,9 @@ public String present() {
   }
 
 
+  public String fhirType() {
+    return resourceName;
+  }
+
+
 }